| Previous changeset 1:500832f27cbc (2015-01-22) Next changeset 3:b24873564cf6 (2016-06-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff |
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modified:
snpEff.xml |
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removed:
.shed.yml |
| b |
| diff -r 500832f27cbc -r e09ce114d240 .shed.yml --- a/.shed.yml Thu Jan 22 08:28:37 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,3 +0,0 @@ -# repository published to https://toolshed.g2.bx.psu.edu/repos/iuc/snpeff -owner: iuc -name: snpeff |
| b |
| diff -r 500832f27cbc -r e09ce114d240 snpEff.xml --- a/snpEff.xml Thu Jan 22 08:28:37 2015 -0500 +++ b/snpEff.xml Fri Feb 19 08:26:25 2016 -0500 |
| [ |
| b'@@ -4,27 +4,28 @@\n <macros>\n <import>snpEff_macros.xml</import>\n </macros>\n+ <expand macro="requirements" />\n+ <expand macro="stdio" />\n <command>\n <![CDATA[\n- java -Xmx6G -jar \\$SNPEFF_JAR_PATH/snpEff.jar eff \n- -c \\$SNPEFF_JAR_PATH/snpEff.config \n+ java -Xmx6G -jar "\\$SNPEFF_JAR_PATH/snpEff.jar" eff\n+ -c "\\$SNPEFF_JAR_PATH/snpEff.config"\n -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength\n- #if $spliceSiteSize and $spliceSiteSize.__str__ != \'\':\n- -spliceSiteSize $spliceSiteSize\n- #end if\n- #if $filterIn and $filterIn.__str__ != \'no_filter\':\n- $filterIn \n+ #if $spliceSiteSize and str($spliceSiteSize) != \'\':\n+ -spliceSiteSize "$spliceSiteSize"\n #end if\n- #if $filterHomHet and $filterHomHet.__str__ != \'no_filter\':\n- $filterHomHet \n+ #if $annotations and str($annotations) != \'\':\n+ #echo " "\n+ #echo \' \'.join(str($annotations).split(\',\'))\n #end if\n- #if $annotations and $annotations.__str__ != \'\':\n+ #if $filterOut and str($filterOut) != \'\':\n #echo " "\n- #echo \' \'.join($annotations.__str__.split(\',\'))\n+ #echo \' \'.join(str($filterOut).split(\',\'))\n #end if\n- #if $filterOut and $filterOut.__str__ != \'\':\n- #echo " "\n- #echo \' \'.join($filterOut.__str__.split(\',\'))\n+ #if $filter.specificEffects == \'yes\' and $filter.effects:\n+ #for $eff in str($filter.effects).split(\',\'):\n+ -no $eff\n+ #end for\n #end if\n #if str( $transcripts ) != \'None\':\n -onlyTr $transcripts\n@@ -33,51 +34,51 @@\n -interval $intervals\n #end if\n #if $statsFile:\n- -stats $statsFile \n+ -stats $statsFile\n #end if\n- #if $offset.__str__ != \'default\':\n- ${offset} \n+ #if str($offset) != \'default\':\n+ ${offset}\n #end if\n- #if $chr.__str__.strip() != \'\':\n- -chr "$chr" \n+ #if str($chr).strip() != \'\':\n+ -chr "$chr"\n #end if\n- $noLog \n+ $noLog\n #if $snpDb.genomeSrc == \'cached\':\n -dataDir ${snpDb.genomeVersion.fields.path}\n- #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != \'\':\n+ #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != \'\':\n #echo " "\n- #echo \' \'.join($snpDb.extra_annotations.__str__.split(\',\'))\n+ #echo \' \'.join(str($snpDb.extra_annotations).split(\',\'))\n #end if\n- #if $snpDb.regulation and $snpDb.regulation.__str__ != \'\':\n- -reg #echo \' -reg \'.join($snpDb.regulation.__str__.split(\',\'))#\n+ #if $snpDb.regulation and str($snpDb.regulation) != \'\':\n+ -reg #echo \' -reg \'.join(str($snpDb.regulation).split(\',\'))#\n #end if\n $snpDb.genomeVersion\n #elif $snpDb.genomeSrc == \'history\':\n -dataDir ${snpDb.snpeff_db.extra_files_path}\n- #if $snpDb.extra_annotations and $snpDb.extra_annotations.__str__ != \'\':\n- #set xannotations = [\' \'] + $snpDb.extra_annotations.__str__.split(\',\')\n+ #if $snpDb.extra_annotations and str($snpDb.extra_annotations) != \'\':\n+ #set xannotations = [\' \'] + str($snpDb.extra_annotations).split(\',\')\n #echo " "\n #echo \' -\'.join($xannotations)\n #end if\n- #if $snpDb.regulation and $snpDb.regulation.__str__ != \'\':\n- -reg #echo \' -reg \'.join($snpDb.regulation.__str__.split(\',\'))#\n+ #if $snpDb.regulation and str($snpDb.regulation) != \'\':\n+ -reg #echo \' -reg \'.join(str($snpDb.regulation).split(\',\'))#\n #end if\n ${snpDb.snpeff_db.metadata.genome_version}\n- #else \n+ #else\n -download\n $snpDb.genome_version\n #end if\n- $input > $snpeff_'..b'be mutated into another stop codon. e.g.: taA/taG, */* LOW</option>\n+ <option value="TRANSCRIPT">TRANSCRIPT (transcript_variant) The variant hits a transcript. MODIFIER</option>\n+ <option value="REGULATION">REGULATION (regulatory_region_variant) The variant hits a known regulatory feature (non-coding). MODIFIER</option>\n+ <option value="UPSTREAM">UPSTREAM (upstream_gene_variant) Upstream of a gene (default length: 5K bases) MODIFIER</option>\n+ <option value="UTR_3_PRIME">UTR_3_PRIME (3_prime_UTR_variant) Variant hits 3\'UTR region MODIFIER</option>\n+ <option value="UTR_3_DELETED">UTR_3_DELETED (3_prime_UTR_truncation + exon_loss) The variant deletes an exon which is in the 3\'UTR of the transcript MODERATE</option>\n+ <option value="UTR_5_PRIME">UTR_5_PRIME (5_prime_UTR_variant) Variant hits 5\'UTR region MODIFIER</option>\n+ <option value="UTR_5_DELETED">UTR_5_DELETED (5_prime_UTR_truncation + exon_loss_variant) The variant deletes an exon which is in the 5\'UTR of the transcript MODERATE</option>\n+ <option value="NEXT_PROT">NEXT_PROT (sequence_feature + exon_loss_variant) A \'NextProt\' based annotation. Details are provided in the \'feature type\' sub-field (ANN), or in the effect details (EFF). MODERATE </option>\n+\n+ </param>\n+ </when>\n+ </conditional>\n \n <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position">\n <option value="default" selected="true">Use default (based on input type)</option>\n@@ -252,7 +292,6 @@\n <filter>generate_stats == True</filter>\n </data>\n </outputs>\n- <expand macro="stdio" />\n <tests>\n <!-- Check that an effect was added in out VCF -->\n <!-- Check for a HTML header indicating that this was successful -->\n@@ -271,8 +310,6 @@\n <param name="genomeSrc" value="named"/>\n <param name="genome_version" value="testCase"/>\n <param name="udLength" value="0"/>\n- <param name="filterHomHet" value="no_filter"/>\n- <param name="filterIn" value="no_filter"/>\n <param name="generate_stats" value="False"/>\n <param name="filterOut" value="+-no-upstream"/>\n <output name="snpeff_output">\n@@ -290,29 +327,6 @@\n <param name="genomeSrc" value="named"/>\n <param name="genome_version" value="testCase"/>\n <param name="udLength" value="0"/>\n- <param name="filterHomHet" value="+-het"/>\n- <param name="filterIn" value="no_filter"/>\n- <!--\n- <param name="filterOut" value=""/>\n- -->\n- <param name="generate_stats" value="False"/>\n- <output name="snpeff_output">\n- <assert_contents>\n- <!-- Check that NO effects were added since -het is set -->\n- <not_has_text text="EFF=NON_SYNONYMOUS_CODING" />\n- </assert_contents>\n- </output>\n- </test>\n-\n- <test>\n- <param name="input" ftype="vcf" value="vcf_homhet.vcf"/>\n- <param name="inputFormat" value="vcf"/>\n- <param name="outputFormat" value="vcf"/>\n- <param name="genomeSrc" value="named"/>\n- <param name="genome_version" value="testCase"/>\n- <param name="udLength" value="0"/>\n- <param name="filterHomHet" value="no_filter"/>\n- <param name="filterIn" value="+-del"/>\n <!--\n <param name="filterOut" value=""/>\n -->\n@@ -336,8 +350,6 @@\n <param name="genomeSrc" value="named"/>\n <param name="genome_version" value="testCase"/>\n <param name="udLength" value="0"/>\n- <param name="filterHomHet" value="no_filter"/>\n- <param name="filterIn" value="no_filter"/>\n <param name="filterOut" value="+-no-upstream"/>\n <param name="generate_stats" value="False"/>\n <output name="snpeff_output">\n' |